isaSpace::BAMsafeReader Class Reference

BAM file safe reader. More...

#include <isoseqAlgn.hpp>

Public Member Functions
	BAMsafeReader ()=default
	Default constructor.
	BAMsafeReader (const std::string &bamFileName)
	Constructor with file name.
	BAMsafeReader (const BAMsafeReader &toCopy)=delete
	Copy constructor.
BAMsafeReader &	operator= (const BAMsafeReader &toCopy)=delete
	Copy assignment operator.
	BAMsafeReader (BAMsafeReader &&toMove) noexcept
	Move constructor.
BAMsafeReader &	operator= (BAMsafeReader &&toMove) noexcept
	Move assignment operator.
	~BAMsafeReader ()
	Destructor.
std::unique_ptr< sam_hdr_t, BAMheaderDeleter >	getHeaderCopy () const
	Get BAM header.
std::pair< std::unique_ptr< bam1_t, BAMrecordDeleter >, int32_t >	getNextRecord ()
	Get the next BAM record.

Detailed Description

BAM file safe reader.

Temporarily sets read-only on the BAM file while reading from it. This is because I observed that calls to some (unclear which) HTSL BAM file read function very rarely deletes the file instead of reading it. Restores permissions after closing.

Constructor & Destructor Documentation

BAMsafeReader() [1/3]

isaSpace::BAMsafeReader::BAMsafeReader

(

const std::string &

bamFileName

)

Constructor with file name.

Parameters

[in]

bamFileName

BAM file name

BAMsafeReader() [2/3]

isaSpace::BAMsafeReader::BAMsafeReader ( const BAMsafeReader & toCopy )

delete

Copy constructor.

Parameters

[in]

toCopy

object to copy

BAMsafeReader() [3/3]

isaSpace::BAMsafeReader::BAMsafeReader ( BAMsafeReader && toMove )

inlinenoexcept

Move constructor.

Parameters

[in]

toMove

object to move

Member Function Documentation

getHeaderCopy()

std::unique_ptr< sam_hdr_t, BAMheaderDeleter > isaSpace::BAMsafeReader::getHeaderCopy ( ) const

nodiscard

Get BAM header.

Returns a pointer to a copy of the stored BAM header.

Returns

pointer to a copy of the header

getNextRecord()

std::pair< std::unique_ptr< bam1_t, BAMrecordDeleter >, int32_t > isaSpace::BAMsafeReader::getNextRecord ( )

nodiscard

Get the next BAM record.

Returns a pointer to the next BAM record in the file and number of bytes read. The byte count can also be used to test for read success.

Returns

BAM header pointer and byte count

operator=() [1/2]

BAMsafeReader & isaSpace::BAMsafeReader::operator= ( BAMsafeReader && toMove )

noexcept

Move assignment operator.

Parameters

[in]

toMove

object to move

Returns

BAMsafeReader object

operator=() [2/2]

BAMsafeReader & isaSpace::BAMsafeReader::operator= ( const BAMsafeReader & toCopy )

delete

Copy assignment operator.

Parameters

[in]

toCopy

object to copy

Returns

BAMsafeReader object

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The documentation for this class was generated from the following file:

• isoseqAlgn.hpp